{"id":"https://openalex.org/W2891740758","doi":"https://doi.org/10.13016/m2542jc2v","title":"DEVELOPMENT AND OPTIMIZATION OF TOOLS FOR CO-EXPRESSION NETWORK ANALYSES OF HOST-PATHOGEN SYSTEMS","display_name":"DEVELOPMENT AND OPTIMIZATION OF TOOLS FOR CO-EXPRESSION NETWORK ANALYSES OF HOST-PATHOGEN SYSTEMS","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2891740758","doi":"https://doi.org/10.13016/m2542jc2v","mag":"2891740758"},"language":"en","primary_location":{"id":"pmh:oai:drum.lib.umd.edu:1903/20779","is_oa":true,"landing_page_url":"https://doi.org/10.13016/M2542JC2V","pdf_url":"http://hdl.handle.net/1903/20779","source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"type":"dissertation","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/1903/20779","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046124101","display_name":"Vincent Keith Hughitt","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hughitt, Vincent Keith","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5046124101"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6248999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6248999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10890","display_name":"Trypanosoma species research and implications","score":0.20020000636577606,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.019999999552965164,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.7430629730224609},{"id":"https://openalex.org/keywords/pathogen","display_name":"Pathogen","score":0.5552934408187866},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5211979746818542},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39932477474212646},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39229705929756165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3581187129020691},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1977424919605255}],"concepts":[{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.7430629730224609},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.5552934408187866},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5211979746818542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39932477474212646},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39229705929756165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3581187129020691},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1977424919605255},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:drum.lib.umd.edu:1903/20779","is_oa":true,"landing_page_url":"https://doi.org/10.13016/M2542JC2V","pdf_url":"http://hdl.handle.net/1903/20779","source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},{"id":"mag:2891740758","is_oa":false,"landing_page_url":"https://drum.lib.umd.edu/handle/1903/20779","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null},{"id":"doi:10.13016/m2542jc2v","is_oa":true,"landing_page_url":"https://doi.org/10.13016/m2542jc2v","pdf_url":null,"source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"thesis"}],"best_oa_location":{"id":"pmh:oai:drum.lib.umd.edu:1903/20779","is_oa":true,"landing_page_url":"https://doi.org/10.13016/M2542JC2V","pdf_url":"http://hdl.handle.net/1903/20779","source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2891740758.pdf","grobid_xml":"https://content.openalex.org/works/W2891740758.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2042242664","https://openalex.org/W3171658775","https://openalex.org/W3146527086","https://openalex.org/W2772920376","https://openalex.org/W2141876630","https://openalex.org/W2171218749","https://openalex.org/W1924228259","https://openalex.org/W2985063702","https://openalex.org/W3001486935","https://openalex.org/W2591299075","https://openalex.org/W579126005"],"abstract_inverted_index":{"High-throughput":[0],"transcriptomics":[1,202,300],"has":[2,70,303],"provided":[3],"a":[4,44,104,151,168,183,223,262,309],"powerful":[5,263],"new":[6,55],"approach":[7,98,117,170,189,227],"for":[8,99,171,199,269,282,298,314],"studying":[9],"host-pathogen":[10,293,299],"interactions.":[11],"While":[12,67],"popular":[13,65],"techniques":[14,268],"such":[15,92],"as":[16,144,146],"differential":[17,224],"expression":[18],"and":[19,128,196,214,230,243,267,273,278,302],"gene":[20,216],"set":[21,264],"enrichment":[22,109],"analysis":[23,226],"can":[24,52],"yield":[25],"informative":[26],"results,":[27],"they":[28],"do":[29],"not":[30,59],"always":[31],"make":[32],"full":[33],"use":[34],"of":[35,47,79,91,103,110,124,150,160,208,236,249,265,275,288,308,311,323],"information":[36,173],"available":[37],"in":[38,73,178,205,258,305],"multi-condition":[39],"experiments.":[40],"Co-expression":[41],"networks":[42,198,217],"provide":[43,261],"novel":[45,152,215],"way":[46],"analyzing":[48],"these":[49,289],"datasets":[50],"which":[51],"lead":[53],"to":[54,87,120,137,147,156,180,192,220,232,244,291],"discoveries":[56],"that":[57,318],"are":[58],"readily":[60],"detectable":[61],"using":[62],"the":[63,77,89,101,114,122,132,148,158,206,234,239,270,306,321],"more":[64],"approaches.":[66],"significant":[68,280],"work":[69,260],"been":[71],"done":[72],"recent":[74],"years":[75],"on":[76,108,131,238],"construction":[78],"coexpression":[80],"networks,":[81,277],"less":[82],"is":[83,118,190,228],"known":[84,211],"about":[85],"how":[86],"measure":[88,121],"quality":[90,102],"networks.":[93],"Here,":[94],"I":[95,166],"describe":[96,167],"an":[97],"evaluating":[100],"co-expression":[105,161,186,241,276,283],"network,":[106,242],"based":[107],"biological":[111],"function":[112],"across":[113,174],"network.":[115,187],"The":[116,255,286],"used":[119,155,191,231],"influence":[123],"various":[125],"data":[126],"transformations":[127],"algorithmic":[129],"parameters":[130],"resulting":[133,204],"network":[134,176,225],"quality,":[135],"leading":[136],"several":[138,292],"unexpected":[139],"findings":[140],"regarding":[141],"commonly-used":[142],"techniques,":[143],"well":[145],"development":[149],"similarity":[153],"metric":[154],"assess":[157],"degree":[159],"between":[162],"two":[163,200],"genes.":[164],"Next,":[165],"simple":[169],"aggregating":[172],"multiple":[175],"parameterizations,":[177],"order":[179],"arrive":[181],"at":[182],"robust":[184],"\u201cconsensus\u201d":[185],"This":[188],"generate":[193],"independent":[194],"host":[195,240],"parasite":[197],"host-trypanosomatid":[201],"datasets,":[203],"detection":[207],"both":[209],"previously":[210],"disease":[212],"pathways":[213],"potentially":[218],"related":[219],"infection.":[221,324],"Finally,":[222],"developed":[229,257],"explore":[233],"impact":[235],"infection":[237,250],"elucidate":[245],"shared":[246],"transcriptional":[247],"signatures":[248],"by":[251],"different":[252],"intracellular":[253],"pathogens.":[254],"approaches":[256,290],"this":[259],"tools":[266],"rigorous":[271],"generation":[272],"evaluation":[274],"have":[279],"implications":[281],"network-based":[284],"research.":[285],"application":[287],"systems":[294],"demonstrates":[295],"their":[296],"utility":[297],"research,":[301],"resulted":[304],"creation":[307],"number":[310],"valuable":[312],"resources":[313],"understanding":[315],"systems-levels":[316],"processes":[317],"occur":[319],"during":[320],"process":[322]},"counts_by_year":[],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
